it's a little odd, but at the 12th fret my low e, A, D, and G strings are fine, the B string is slighly flat and the top E string is very flat, about half a semitone out. It's annoying for soloing.

I have already done that intonation thing at the bridge, and the E and B strings are intonatred as far as they will go but it's still not enough....

What can I do.....?
It's always a compromise. You could do fanned frets or they even do guitars where the location of the fret is filed from string to string, but you kinda have to live with it otherwise.
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i had that problem i took it into a shop i dont know what the did but the fixed it
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Squiers do have that problem. Get a new guitar if it bothers you overmuch. A better guitar. Pay more than £200 if possible.
you could try changing string gauge see if your able to intonate it that way, but maybe having it properly set up would be best, it should only cost around £15 ish
Its not the brand or price. The squires are made in china now or at least the one I have is. And it plays and intonates fine. But I have a copy of a strat (it says fender stratocaster but has no serial number). And the heavy e string is way out on intonation. I checked and the neck socket isnt right. So the neck goes into the guitar further than its supposed to. You can use a tape measure to see the scale length from nut to saddles. It should be 25 1/2 with some room for the saddles to go back. If all your saddles are pretty far back thats probably your problem. I had to take the saddle out and cut the spring and the screw down so the saddle could move further back. Or maybe it was an off day at the plant and they didnt do the frets right. And paying more money may or may not get you a better guitar. Epi's, hamer, and many other brands are made there now.
The saddles are as far forward as I can make them on the E and B strings.... that's why I have a problem.

So I wil probabaly take it into a shop to get a setup.

But If was going to try different guage strings, would I want a heavier or lighter guage? I use 10s at the moment.